Fragile X Syndrome Case File

Fragile X Syndrome Case File

Eugene C.Toy, MD, William E. Seifert, Jr., PHD, Henry W. Strobel, PHD, Konrad P. Harms, MD

❖ CASE 13

An 8-year-old boy is brought to his pediatrician by his mother because she was concerned that he was having language-speech problems, was hyperactive, and was told by teachers that he may have mental retardation. The mother reports a strong family history of mental retardation in males. The boy on exam is found to have a large jaw, prominent ears, and enlarged testes (macroorchidism). The mother was told her family had a genetic problem causing the mental retardation. The patient underwent a series of blood tests and was scheduled to see a genetic counselor, who expressed that the etiology of the genetic defect was likely transmitted from his mother. The genetic counselor states that his mother likely has a silent mutation.

◆ What is the most likely diagnosis?

◆ Which chromosome is likely to be affected?

◆ What are some types of biochemical mutations?

◆ What is the biochemical basis of the different types of mutations?

ANSWERS TO CASE 13: FRAGILE X SYNDROME

Summary: An 8-year-old boy has mental retardation, speech-language problems, hyperactivity, physical findings of large jaw, prominent ears, and macroorchidism and has a strong family history of mental retardation. The genetic counselor informs the mother that she is the carrier and that she has a silent mutation.

◆ Most likely diagnosis: Fragile X syndrome (most common form of familial mental retardation).

◆ Affected chromosome: Chromosome X

◆ Types of mutations: Silent means protein product not affected; missense means single amino acid substitution leading to significant alteration (such as sickle cell); and nonsense means that a stop codon is formed.

◆ Molecular basis of disease: Mutation resulting in an increased number of CGG repeats on the X chromosome. When the number of repeats reaches a critical size, it can be methylated and inactivated resulting in the disorder. Individuals who carry 50 to 199 repeats are phenotypically normal and carry a premutation. If repeats exceed 200, the patient has a full mutation; and if methylation occurs, he or she will be affected.

CLINICAL CORRELATION

Fragile X is the most common inherited form of mental retardation, affecting primarily males. The clinical presentation can vary, but usually the affected male has moderate to severe mental retardation, hyperactivity, typical facies such as large jaw and large ears. Pigmented skin lesions (café au lait) can also be seen. Because females have two copies of the X chromosome, they are “resistant” to mutations on one gene. Fragile X affects the long arm of the X chromosome, with multiple copies of triplicate repeats, usually CGG, leading to methylation of the deoxyribonucleic acid (DNA). The fragile X mental retardation (FMR) gene product is affected and, through a little-understood mechanism, leads to mental retardation.

APPROACH TO MUTATIONS

Objectives

1. Know the definitions of point mutations (silent, missense, and nonsense), insertions, deletions, and frameshift mutations.

2. Be familiar with the defect in fragile X syndrome.

Definitions

Point mutation: The substitution of a single nucleotide in the genetic material of an organism. These include silent, missense, and nonsense mutations.

Silent mutation: A single nucleotide is exchanged by another, but this alteration does not change the amino acid for which the codon codes. The final protein product remains unchanged.

Missense mutation: A single nucleotide is exchanged by another, and this alteration does have an effect on the coding amino acid. The final protein product is also modified. The modification may or may not be deleterious to the final protein, depending on the function of the amino acid.

Nonsense mutation: A single nucleotide is exchanged by another, which produces a new stop codon at this position. This premature stop codon generally results in a truncated form of the protein and most often leaves it as an inactive form.

Deletion: One or more nucleotides are removed from the genetic sequence. If the deletions are multiples of one or two, a frameshift will be the result, which will likely damage the final protein product. A deletion of three or a multiple of three does not shift the reading frame, rather it would merely remove a codon(s). The final protein product would lose amino acid(s), which may or may not leave it inoperative.

Insertion: One or more nucleotides are added to the genetic sequence. These are the opposite of deletions.

Trinucleotide repeat expansion: Amplification from one generation to the next of three nucleotide repeats in the coding or noncoding regions of DNA. The mechanism may arise from DNA complimentary strand slippage. This is associated with fragile X syndrome and myotonic dystrophy.

DNA methylation: Process by which methyl groups are added to DNA bases (most often cytosine). Methylation functions to regulate gene expression because heavily methylated genes are not expressed. Also, bacteria use methylated DNA as a defense mechanism. Every organism has different patterns of methylated DNA, and bacteria take advantage of this by destroying foreign DNA via nucleases, enzymes that cut DNA at specific sites.

DISCUSSION

Replication often produces changes in the chemical makeup of DNA. Many of these changes are easily repaired; however, those alterations in the DNA base sequence that do not get repaired are referred to as mutations. There are various types of mutations including point mutations, deletions, and insertions. subdivided into three categories; silent, missense, and nonsense. Silent mutations do not affect the translated mRNA or final protein product— thus the name silent. The genetic code is degenerate, which means that most amino acids are encoded by several different codons or triplets of DNA/RNA bases. Therefore, it is possible to switch a single base but not alter the resulting protein product (Table 13-1a). The sickle cell trait is a result of a missense mutation. This type of point mutation actually does alter the protein product. In the case of sickle cell hemoglobin, an adenine is replaced by a thymine, causing a hydrophilic glutamic acid to be replaced with a hydrophobic valine in the resulting protein (Table 13-1b). In a nonsense mutation, the mutation brings about a premature stop in the gene of interest because the altered codon now represents a stop codon (Table 13-1c). These are commonly seen in muscular dystrophies and some cystic fibrosis cases. Aminoglycosides are currently being used to treat premature stop codons as they affect the translational accuracy of transfer ribonucleic acids (tRNAs), thereby allowing recognition of incorrect codons including the stop codon. Ultimately, the translation machinery reads through the premature stop codon because of altered amino acid insertion by the tRNAs and produces full-length protein instead of a truncated protein or degraded mRNA.

Table 13-1a

EXAMPLES OF MUTATIONAL EVENTS

SILENT MUTATION

Table 13-1b

MISSENSE MUTATION

Table 13-1c

NONSENSE MUTATION

Another type of mutation is a deletion in which one or more DNA bases have been removed. However, an insertion is a mutation wherein one or more DNA bases have been added. These two types of mutations can cause a shift in the open reading frame, called frameshift mutations, of a gene if the insertion or deletion is a multiple of one or two bases. Typically, a frameshift mutation will result in disease either as result of altering the protein product, leaving it nonfunctional, or generation of a premature stop codon, which confers a truncated form of the altered protein (Table 13-2). Both cases present major problems because the altered protein will not likely be able to carry out the normal duties required of it. Since codons are read as multiples of three, an insertion or deletion of three or a multiple of three may or may not be as deleterious to the gene as multiples of one or two. In this situation, the resulting protein could include extra amino acids in the case of insertions or lose amino acids in the case of deletions. It is possible that this could hinder the protein from normally functioning.

Table 13-2

FRAMESHIFT MUTATION

Many forms of fragile X syndrome are examples of insertions in multiples of three where the outcome is detrimental not because of altered amino acid sequence but rather a loss of protein expression. Deletions and insertions typically occur in highly repetitive sequences, and this is exactly what is seen in fragile X. Fragile X syndrome is the most common form of inherited mental retardation. It affects approximately 1 in 4000 males and 1 in 8000 females. Mutations of the X chromosome, including fragile X, may account for the higher number of male patients in mentally handicapped facilities. The fragile X mental retardation 1 (FMR1) gene is highly conserved. Normal individuals have 7 to 60 (CGG) repeats in the 5′-untranslated region, and the repeats are often broken up by AGG. Many fragile X individuals have an increase in the number of CGG repeats, which may expand to over 230 repeats. This is termed the full mutation. Repeats ranging from 60 to 230 are called a premutation. The premutation carrier has normal fragile X mental retardation protein (FMRP) levels, but the gene is unstable in its passage to offspring.

The fragile X phenotype is mainly caused by the loss of FMRP resulting from CGG trinucleotide repeat expansion of the FMR1 gene. However, some point mutations and deletions in the FMR1 gene show the same phenotype as the repeat expansion. The alteration arising from the trinucleotide repeat expansion within the promoter region of FMR1 leads to enhanced local methylation and ultimately transcriptional silencing. DNA methylation causes protrusions in the DNA helix where the methylated cytosines interfere with transcription factor binding. This is a common property used for gene regulation. However, in the case of fragile X, the methylation signals to halt all expression of FMRP. Loss of FMRP gives the phenotypical characteristics commonly seen in fragile X patients.

COMPREHENSION QUESTIONS

[13.1] A 6-year-old boy visits his physician because his parents have noticed autistic behavior and speech problems. The mother’s family does have a history of mental retardation. Therefore, the physician suggested a genetic screen of the fragile X mental retardation 1 (FMR1) gene for fragile X syndrome. Polymerase chain reaction (PCR) revealed borderline fragile X syndrome. What situation most likely explains this result?

A. A complete loss of fragile X mental retardation protein (FMRP)

B. An FMR1 gene CGG repeat expansion of 60 with partial DNA methylation

C. An FMR1 gene CGG repeat expansion of 230 with minor DNA methylation

D. An FMR1 gene CGG repeat expansion of 280 with complete DNA methylation

[13.2 to 13.3] Use the genetic code for Questions [13.2] and [13.3].

Using the genetic code above, predict the type of mutation that had to occur to show these alterations in the final protein product for Questions [13.2] and [13.3]:

[13.2]

A. Missense mutation

B. Nonsense mutation

C. Silent mutation

D. Repeat expansion

[13.3]

A. Deletion of G in third codon

B. Deletion of A in second codon

C. Insertion of T between second and third codons

D. Insertion of GT between AC and A of second codon

Answers

[13.1] C. A CGG repeat expansion of 230 base pairs is just at the limit of the number of repeats required to have the full mutation. Expansions from 7 to 60 are seen in normal patients and those exceeding 230 are positive for fragile X syndrome. Because some of the DNA was methylated, this could help to silence the expression of FMRP and cause some of the phenotype seen in the patient. Therefore, this scenario would be considered borderline fragile X.

[13.2] B. A nonsense mutation causes a premature stop codon on a single nucleotide substitution. The original sequence, TAT, coding for a tyrosine, must have been mutated to either TAA or TAG, leaving a stop codon in place of the tyrosine.

[13.3] A. Deletion of G in the third codon gives the sequence:

TTT ACC GTT TAT CTA GGG ATG →

TTT ACC TTT ATC TAG GGA TG

This causes a frameshift and a premature stop codon to be generated. Therefore, the final protein product would look like the one in question.

BIOCHEMISTRY PEARLS

❖ Mutations are alterations in the DNA base sequence that do not get repaired.

❖ There are various types of mutations including point mutations, deletions, and insertions.

❖ Point mutations arise when one base pair is substituted by another, and they are the most common types of mutations.

❖ Point mutations can be further subdivided into three categories: silent, missense, and nonsense.

❖ Many fragile X individuals have an increase in the number of CGG repeats, which may expand to over 230 repeats.

References

Crawford DC, Acuna JM, Sherman SL. FMR1 and the fragile X syndrome: human genome epidemiology review. Genet Med 2001 Sep–Oct;3(5):359–71. 

Warren ST, Sherman SL. The fragile X syndrome. In: Scriver CR, Beaudet AL, Sly WS, et al., eds. The Metabolic and Molecular Basis of Inherited Disease, 8th ed. New York: McGraw-Hill, 2001.

HomeCase FilesFragile X Syndrome Case File